Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.

🦠🧫 a collaboration with the Institute for Tropical Medicine in Tübingen and CERMEL in Gabon @cmfi.bsky.social

Asexuality is a global identity. That’s a major finding in a study I recently published with @francescorampazzo.com in Demographic Research. Analyzing dating app data spanning 162 countries from over 900,000 users, we found that asexuality showed up in every age group and in every region.

MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...

We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes. Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8

It’s not only medications—environmental chemicals can also inadvertently harm our gut microbes. Excited to have contributed a bit to this important study!

🚨‼️ New paper alert! ‘Sewers to Seas: exploring pathogens and antimicrobial resistance on microplastics from hospital wastewater to marine environments’ FULL ARTICLE: www.sciencedirect.com/science/arti... ➡️ Check out @pml.ac.uk’s coverage: pml.ac.uk/news/micropl...

Great to see our @exeter.ac.uk and @pml.ac.uk research highlighted in @uk.theconversation.com 🤟🙏 ➡️ theconversation.com/plastic-bio-...

Are you looking for a wild PhD opportunity? 🦠🧵 There are several opportunities to join the Wild Microbiome Lab in 2026! Scroll for more information, or visit the link below for full project descriptions and application information👇 xavharrison.github.io

Exciting PhD position on algal-driven metal remediation with Dr Michiel Vos and collaborators at the University of Exeter. This project combines plant and microbial ecology, and geochemistry to develop innovative biological solutions for metal pollution www.findaphd.com/phds/project...

📢 New paper in @natcomms.nature.com Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes doi.org/10.1038/s414... Thrilled to share this massive global effort led by H.M. Martiny, @patrickmunk.bsky.social, F. Aarestrup & the Global Sewage Consortium

A lot has happened since our first announcement of #ExE2026, an evolutionary ecology conference hosted by @uniexecec.bsky.social in #Cornwall from June 29 to July 3 2026. Have a look at our new website to see our confirmed plenary speakers, the mid-conference excursions, and more. 👉 evoxeco.uk 👈

Imagine we could travel back in time ⏪⌛️to explore the world of bacterial pathogens before humans discovered and industrialised antibiotics We just did that to study the history of #AMR spread @science.org doi.org/10.1126/scie... If you like time travel & biology, this 🧵is for you👇

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)! We're looking for someone keen on bioinformatics and microbiome evolution. Important info below on eligibility & URSA competition funding👇 www.findaphd.com/phds/project...

Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published! proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...

We have a new preprint modeling the regulatory networks of efflux pumps to predict the evolution of multidrug resistance in P. aeruginosa. Also explore cross-resistance, collateral sensitivity & loss of resistance. With @suvamroy.bsky.social @elibbyscience.bsky.social www.biorxiv.org/content/10.1...

🚨#PhD studentship opportunity! Plasmids provide bacteria with antimicrobial resistance, but do they have more fundamental effects on behaviour? 🧫🦠💫🧟‍♂️ Apply for a 4y funded MRC DiMeN position with me and Jamie Wheeler @livuni-ives.bsky.social www.findaphd.com/phds/project...

PhD studentship opportunity! Join us at St Andrews to study the factors controlling plasmid transmission in the gut. Competition-funded as part of the EASTBIO DTP, co-supervised with Dr Jaclyn Pearson. Please share & pass on to anyone interested! 🦠🧫 Deadline 15th December👇

‘The latest surveillance data found that the number of antibiotic-resistant infections in 2024 equated to an average of nearly 400 newly reported cases a week.’ www.theguardian.com/society/2025...

**PhD opportunity @uniexecec.bsky.social** How is immunogenetic variation maintained in the wild? Why are alleles that increase disease susceptibility maintained in populations, when natural selection should eliminate them?

Our contribution to this special issue: a review on data analysis of human gut microbiome data from global populations www.cell.com/trends/micro...

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

A glitch in the matrix? No! I have another PhD available on temperature and AMR, this time with @swbiodtp.bsky.social. Join a friendly group (padpadpadpad.netlify.app/about) in Cornwall to do evolutionary ecology, experimental evolution, and combine phenotyping and sequencing. 🧪🦠 #microsky

Strain displacement in microbiomes via ecological competition www.nature.com/articles/s41... #jcampubs

Functional redundancy matters: the more overlapping microbial functions you have, the more resilient your #microbiome. We showed a strong negative correlation between redundancy loss and increase in #antimicrobial resistance protein upon #drug treatment of microbiomes. @quadraminstitute.bsky.social

Are you, or someone you know, looking for a PhD, starting in Oct 2026? Do you like bacteria, genomics & puzzles?🦠🧬🧩 Do you wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social? Please apply or share by 2 Dec 🗓️ #PhDposition #academicsky Find out more ⬇️

Countless drugs & chemicals now coexist in the environment, mixtures "that may be quietly shaping the evolution of antibiotic resistance." The fantastic Dr April Hayes explains how: theconversation.com/growing-cocktail-of-medicines-in-worlds-waterways-could-be-fuelling-antibiotic-resistance-266945

I wrote a piece for The Conversation that came out today focused on our new study but also in general about mixtures of drugs in the environment and what that could mean for AMR - theconversation.com/growing-cock...

how do non-antibiotic drugs act in mixture with ciprofloxacin? we found in our recent study doi.org/10.1093/isme... that these NADs enhance selection for AMR within complex bacterial communities. we tested this mixture at environmental concs, and identified effects on growth, intI1, and other genes

Research assistant + postdoc position on a NERC funded project working w @darrenobbard.bsky.social and collaborating with @savebutterflies.bsky.social on the ecological and evolutionary drivers of the virome of UK moths @uniexecec.bsky.social. Descriptions below and links here benlongdon.com/join/

what postdocs actually want: - to not have their grants canceled - reasonable chances at getting an academic position - job security - a thriving private sector so the entire research system can flourish <3 higher ed institutions in 2025: - best i can do is an origami night

cool phd position with a really great PI and associated supervisory team alert

📢🚨 Check out @drgdavidson.bsky.social's 3-year senior PDRA role below @uniofeastanglia.bsky.social! Super exciting project exploring wildlife ecology 🐾 and gut microbiome bioinformatics 🧬! 👉 Apply: vacancies.uea.ac.uk/vacancies/18... 💬 Informal enquiries to Gabrielle welcome!

If you generate or reuse #microbiome data, check out these guidelines for equitable sequence data reuse. Grateful to @alexjprobst.bsky.social and his team for leading this important work and for bringing together 160+ microbiome scientists (myself included) to contribute! doi.org/10.1038/s415...

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n

Join myself and others in Exeter, alongside artist Steve McCracken, for a curated trail of art and science. Get real time insights into pollution while spotting new artworks of birds. @ecehh.org www.eventbrite.co.uk/e/walking-to...

Open postdoc position in in my lab in Berlin @mpiib-berlin.mpg.de. Join us to push the frontier in ancient microbial genomics. Please apply until Oct 17th. Reach out in case you have any questions. www.mpiib-berlin.mpg.de/2193291/job_...

www.cell.com/cell/fulltex... #microsky #microbiome

more exciting work showing the effects that non-antibiotic pharmaceuticals can have on microbial communities 🦠🧫💊

Finding microbes in cancer sequencing data has been controversial. Are we seeing real biology… or just contamination + batch effects?

🤩🎢 #MVIF Season 5 is just about to start! Ten #microbiome events, free to attend, great to present your latest results. #ECR, #preprints, unpublished work are welcome! 👉 www.microbiome-vif.org All talks get a DOI, and those associated with preprints are added to their #bioRxiv #medRxiv pages too.

PhD opportunity, please share: We are looking for a prospective PhD student to start in October 2026 who is excited about bacteria (Klebsiella pneumoniae), how they interact, and how they exchange DNA. All details can be found on the funder website 👉 gw4biomed.ac.uk/developing-c...

New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards. We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...

💊 Non-antibiotic drugs & resistance A new study shows common medicines like ibuprofen and acetaminophen can boost E. coli resistance to antibiotics, raising concerns for aged care settings. 🔗 www.nature.com/articles/s44... #SciComm 🧪 #AMR

I'm super bummed to be missing #ESEB2025 @eseb2025.bsky.social due to a cancelled flight! Here's a quick overview of my talk "Gene- and genome-focused perspectives on microbial pangenomes" slated to be part of The Evolution of Microbial Pangenomes -- which I recommend you attend tomorrow (Fri) ! 1/n

If you ever find yourself needing evidence for ‘Plasmids are just as common in microbes without resistance genes,’ we’ve got you covered! Check our new paper, out today: www.microbiologyresearch.org/content/jour...

Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com! We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨ Huge team effort! www.nature.com/articles/s41...

I often say that reporting on sex testing in sports is like reporting on a really twisted, 100 year game of wack-a-mole where we see the same things happen over and over. This is a great example. (A short thread, if you'll indulge me.)

Check out this incredible analysis! Prehistoric Global Migration of Vanishing Gut Microbes With Humans www.biorxiv.org/content/10.1...